Strain identifier

BacDive ID: 13758

Type strain: Yes

Species: Roseivivax halotolerans

Strain history: CIP <- 1999, Y. Nishimura, Tokyo Univ., Tokyo, Japan: strain Och 210 <- Shiba

NCBI tax ID(s): 93684 (species)

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General

@ref: 5954

BacDive-ID: 13758

DSM-Number: 15490

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Roseivivax halotolerans DSM 15490 is a mesophilic bacterium that was isolated from epiphytes on the stromatolites of a saline lake.

NCBI tax id

  • NCBI tax id: 93684
  • Matching level: species

strain history

@refhistory
5954<- JCM <- Y. Nishimura <- T. Shiba; OCh 210
67770Y. Nishimura <-- T. Shiba OCh 210.
119829CIP <- 1999, Y. Nishimura, Tokyo Univ., Tokyo, Japan: strain Och 210 <- Shiba

doi: 10.13145/bacdive13758.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Roseivivax
  • species: Roseivivax halotolerans
  • full scientific name: Roseivivax halotolerans Suzuki et al. 1999

@ref: 5954

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseivivax

species: Roseivivax halotolerans

full scientific name: Roseivivax halotolerans Suzuki et al. 1999

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.509
6948099.998negative
119829nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5954BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
5954PPES-II AGAR MEDIUM (DSMZ Medium 1075)yeshttps://mediadive.dsmz.de/medium/1075Name: PPES-II AGAR MEDIUM (DSMZ Medium 1075) Composition: NaCl 30.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 10.8 g/l MgSO4 x 7 H2O 5.4 g/l Peptone 2.0 g/l Proteose peptone no. 3 1.0 g/l Soytone 1.0 g/l Yeast extract 1.0 g/l CaCl2 x 2 H2O 1.0 g/l KCl 0.7 g/l Fe(III)-EDTA 0.1 g/l Distilled water
40257Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119829CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5954positivegrowth30mesophilic
5954positivegrowth28mesophilic
40257positivegrowth30mesophilic
67770positivegrowth27mesophilic
119829positivegrowth15-41
119829nogrowth5psychrophilic
119829nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.993

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1198294853esculin+hydrolysis
119829606565hippurate-hydrolysis
11982917632nitrate-builds gas from
11982917632nitrate-reduction
11982916301nitrite-builds gas from
11982916301nitrite-reduction
11982917234glucose-degradation

metabolite production

  • @ref: 119829
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119829oxidase+
119829beta-galactosidase+3.2.1.23
119829alcohol dehydrogenase-1.1.1.1
119829gelatinase+
119829amylase-
119829caseinase+3.4.21.50
119829catalase+1.11.1.6
119829tween esterase-
119829gamma-glutamyltransferase-2.3.2.2
119829lecithinase-
119829lipase-
119829lysine decarboxylase-4.1.1.18
119829ornithine decarboxylase-4.1.1.17
119829phenylalanine ammonia-lyase+4.3.1.24
119829protease+
119829tryptophan deaminase-
119829urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119829-+++-+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5954epiphytes on the stromatolites of a saline lakeLake CliftonAustraliaAUSAustralia and Oceania
67770Epiphytes on the stromatolites
119829CharophyteClifton lakeAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Host#Other#Epibiont
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_138390.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_23853;97_68782;98_92150;99_138390&stattab=map
  • Last taxonomy: Roseivivax halotolerans subclade
  • 16S sequence: DQ915622
  • Sequence Identity:
  • Total samples: 421
  • soil counts: 72
  • aquatic counts: 310
  • animal counts: 37
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59541Risk group (German classification)
1198291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Roseivivax halotolerans strain NBRC16686 16S ribosomal RNA gene, partial sequenceDQ9156221307ena93684
5954Roseivivax halotolerans gene for 16S rRNA, strain: OCh 210D858311372ena93684

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseivivax halotolerans strain JCM 1027193684.8wgspatric93684
66792Roseivivax halotolerans DSM 154902675903164draftimg93684
67770Roseivivax halotolerans JCM 10271GCA_900115815contigncbi93684

GC content

@refGC-contentmethod
595459.7
6777059.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno69.349no
flagellatedno88.93no
gram-positiveno97.999no
anaerobicno96.33no
halophileyes84.474no
spore-formingno96.352no
glucose-utilyes74.649no
aerobicyes82.069no
thermophileno94.126no
glucose-fermentno89.564no

External links

@ref: 5954

culture collection no.: DSM 15490, ATCC 700842, CIP 105984, IFO 16686, JCM 10271, NBRC 16686, OCh 210, BCRC 80019

straininfo link

  • @ref: 82939
  • straininfo: 46979

literature

  • topic: Phylogeny
  • Pubmed-ID: 10319485
  • title: Roseivivax halodurans gen. nov., sp. nov. and Roseivivax halotolerans sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from a saline lake.
  • authors: Suzuki T, Muroga Y, Takahama M, Nishimura Y
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-2-629
  • year: 1999
  • mesh: Bacteria, Aerobic/*classification/cytology/isolation & purification/physiology, Bacteriochlorophylls/*analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5954Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15490)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15490
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40257Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18063
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82939Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46979.1StrainInfo: A central database for resolving microbial strain identifiers
119829Curators of the CIPCollection of Institut Pasteur (CIP 105984)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105984